Antigen-driven detection and treatment of coccidioidomycosis

ABSTRACT

Materials and methods for detecting and treating Coccidioidomycosis (Valley Fever) are provided herein. For example, materials and methods for enriching and detecting biomarker antigens (e.g., polypeptides and/or glycans) from Coccidioides immitis and Coccidioides posadasii, the fungi that cause Valley Fever, are described herein, as are methods for treating an individual for Valley Fever based on the results of the described detection methods.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a National Stage application under 35 U.S.C. § 371of International Application No. PCT/US2017/037866 having anInternational Filing Date of Jun. 16, 2017, which claims benefit ofpriority from U.S. Application Ser. No. 62/351,073, filed on Jun. 16,2016.

TECHNICAL FIELD

This document relates to materials and methods for detecting andtreating Valley Fever.

BACKGROUND

Coccidioidomycosis [Valley Fever (VF)] is a respiratory disease causedby the inhalation of spores from the soil-dwelling fungi, Coccidioidesimmitis and Coccidioides posadasii. VF is endemic to the SouthwesternU.S. and northern Mexico. In 2012, for example, 73% of the casesreported in the U.S. were reported in Arizona, and 25% were reported inCalifornia. The occurrence of VF has increased dramatically since thelate 1990's. About 40% of affected individuals experience symptoms suchas cough, fever, fatigue, rash, and night sweats, and about 5% havesevere pneumonia and require appropriate treatment. In fact, VF has beenreported to cause up to 30% of community-acquired pneumonia (CAP) inendemic regions (Blair et al., Emerg Infect Dis 20(6):983-990, 2014).Further, in about 1% of individuals infected with VF, the organismdisseminates from the lungs to other parts of the body, causing alife-threatening systemic infection. Primary infection or reactivationof latent infection are higher risks in patients who areimmunocompromised (e.g., transplant recipients or people with AIDS), orwho are taking immune-modifying drugs such as TNF-α inhibitors.

In the environment, Coccidioides spp. exists as a mold with septatehyphae, which fragment into arthroconidia that are easily aerosolized.These arthroconidia are inhaled and settle into the lungs, eventuallybecoming spherules that divide internally until they are filled withendospores. When the spherules rupture, the endospores are released,disseminating into surrounding tissue and developing into new spherulesthat repeat the cycle.

SUMMARY

Diagnosing VF from symptoms alone can be difficult, if not impossible,due to similarities between the symptoms of VF and symptoms associatedwith CAP caused by other organisms. Unlike many other etiologies of CAP(bacteria and viruses) that are either self-limited or treatedempirically, VF is not responsive to antibacterial or anti-viral drugs,and symptoms may persist for months. The mean time to diagnosis of VF isabout 2-3 months (Sunenshine et al., Ann NY Acad Sci 1111:96-102, 2007),a time period that may include one or more empiric antibacterial oranti-viral therapy regimens in the setting of persisting or worseningsymptoms and often multiple visits to a healthcare facility. VF istypically not high in the differential diagnosis, so testing is oftennot performed. This is true even in endemic areas, since physicianspracticing in such locations are likely to have been trained innon-endemic areas and are not familiar with recognizing the disease ortesting strategies.

Moreover, even when VF testing is performed, antibodies against thefungus may not be produced at detectable levels by the body for 4-10weeks. Therefore, early negative test results may occur and repeatedantibody testing may be performed. Even though there are three methodsof antibody detection (complement fixation [CF], immunodiffusion [ID],and enzyme immunoassay [EIA]), not all patients with VF will testpositive by all antibody assays. Some patients fail to ever mount anantibody response, rendering antibody assays useless. Antibody testingis only a proxy of disease and immunity, since the functionallyeffective immune response is cell-mediated, rather than via antibodies(humoral response). Positive results by antibody tests may persist wellafter clinical improvement. Thus, when a complex patient (e.g., atransplant recipient) is being treated, it can be difficult to gaindefinitive laboratory evidence of disease resolution, particularly whennon-specific symptoms consistent with VF or other diseases remain.Culture is inexpensive but slow (ranging from several to many days), andPCR is rapid but expensive. Culture and PCR have similar sensitivity,but both are limited in that they require a sputum or bronchoalveolarlavage (BAL) specimen to send to the laboratory. Most patients with VFhave a dry cough and are not able to produce sputum, obviating theutility of culture and PCR.

Thus, this document provides improved methods for detecting and treatingVF, based at least in part on the discovery that direct detection offungal components (as opposed to detection of antibodies) from bodyfluids can provide a definitive diagnosis. As described herein, forexample, certain lectins (carbohydrate-binding proteins) havedifferential binding properties to coccidioidal antigens (polypeptidesand/or glycans), due to the fact that many fungal glycosylation patternsare distinct from mammalian glycosylation patterns. These differentialbinding properties can serve as a tool for improved detection andtreatment of VF. Thus, this document is based, at least in part, on theidentification of a common subset of polypeptide and/or glycan antigensthat are found in patients with active VF that bind to particularlectins [Griffonia simplicifolia II lectin (GSLII) and/or succinylatedWheat Germ Agglutinin (sWGA)] and/or antibodies specific to Coccidioidesantigens, but are not found in control patients (e.g., healthy subjectsor patients known to have non-coccidioidal community-acquiredpneumonia). The lectins and/or antibodies may be used in an enzymeimmunoassay format, or to partially purify antigens for detection by amass spectrometry assay such as matrix associated laser desorptionionization-time of flight (MALDI-TOF) mass spectrometry.

In some embodiments, therefore, this document provides assays thatinclude detecting antigens from C. immitis and/or C. posadasii, thecausative agents of VF. The assays utilize lectins to selectively purifyfungal antigens (e.g., peptides and/or glycans) from body fluids such asblood, plasma, serum, urine, bronchoalveolar lavage, saliva, etc. Thelectin approach can be useful because glycosylation patterns may bequite specific to particular species or organisms. For example, proteinsfrom fungal organisms often have mannose-rich glycosylation, whereashuman proteins often have terminal sialic acid residues in theircarbohydrate groups. The methods provided herein use mass spectrometryfor sensitive and specific detection of the fungal antigens (e.g.,polypeptides and/or glycans). In some cases, the methods can be adaptedto include the use of MALDI-TOF mass spectrometry of the type employedfor rapid and low cost identification of bacteria from culture plates(e.g., from Bruker Daltonics, Billerica, Mass., and BioMérieux,Marcy-l'Étoile, France).

In one aspect, this document features a method for tailoring or alteringtreatment for a subject presenting with, and optionally undergoingantimicrobial treatment for, one or more symptoms of community-acquiredpneumonia, or a subject with one or more symptoms of invasive fungalinfection. The method includes detecting one or more antigens (e.g.,polypeptides and/or glycans) of Coccidioides immitis and/or Coccidioidesposadasii in a body fluid sample from the subject, wherein the detectingincludes lectin-based or antibody-based enrichment of C. immitis and/orC. posadasii antigens, and detection of one or more of the antigens; andstopping the antibacterial or anti-viral treatment, initiatingantifungal treatment, or stopping the antibacterial or anti-viraltreatment and initiating antifungal treatment. The antifungal treatmentcan include administration of fluconazole, ketoconazole, itraconazole,voriconazole, posaconazole, isavuconazole, amphotericin, or otheravailable antifungal agents. The detecting can include the use of commonimmunoassay formats, such as enzyme immunoassay (EIA), enzyme-linkedimmunoabsorbant assay (ELISA), line immunochromatographic assays (LIAs),and the like, whereby an antibody is immobilized on a surface (e.g.,plastic or a paper filter), and a body fluid or affinity-enriched bodyfluid is contacted with the immobilized antibody and then detected byanother binding agent (e.g., antibody or lectin). The detecting also caninclude using mass spectrometry. The mass spectrometry can generatemass/charge peaks that are representative for infection withCoccidioides fungus, or that supply data that include sequences ofpeptides or evidence of glycan structures that match Coccidioidessequences/structures. The mass spectrometry can be matrix associatedlaser desorption ionization time of flight (MALDI-TOF) massspectrometry, or liquid chromatography followed by tandem massspectrometry (LC-MS/MS). The detecting can include using one or moreantibodies against one or more Coccidioides antigens (e.g., peptidesand/or glycans). The detecting can include using one or more lectinsthat bind to the one or more antigens. The one or more lectins can besuccinylated Wheat Germ Agglutinin (sWGA), Griffonia simplicifolia IIlectin (GSLII), Wheat Germ Agglutinin (WGA), or a combination of WGA,sWGA, and/or GSLII, or other lectins that bind exclusively toCoccidioides antigens such as N-acetyl glucosamine (GlcNAc). Thedetecting can include using one or more lectins that bind to both humanand Coccidioides antigens. The one or more lectins can be Concanavalin A(Con A), Erythrina crystagalli Lectin (ECL), and Pisum sativumAgglutinin (PSA). The lectin can bind to human antigens and negativelyenrich Coccidioides antigens by reducing the number or percentage ofhuman antigens present in the body fluid from the subject. In someembodiments, the negatively enriching lectin can include one or more ofCon A, Datura stramonium Lectin (DSL), ECL, Griffonia simplicifoliaLectin I (GSLI), Jacalin (JAC), Len culinaris Lectin (LCA), PeanutAgglutinun (PNA), Phaseolus vulgaris Erythroagglutinin (PVE), Phaseolusvulgaris Leukoagglutinin (PVL), PSA, Ricinus communis Agglutinin (RCAI), Solanum tuberosum Lectin (STL), Soybean Agglutinin (SBA), Ulexeuropaeus Agglutinin I (UEA I), and Vicia villosa Lectin (VVL). The bodyfluid can include blood, plasma, serum, urine, saliva, sputum, inducedsputum, nasal washing, bronchial washing, bronchial brushing, trachealsecretions, bronchoalveolar lavage, or cerebrospinal fluid. The volumeof the body fluid sample can range from 0.02 mL to 200 mL. The bodyfluid sample can be contacted with the lectin(s) for 1 second to 48hours.

In another aspect, this document features a method for altering thetreatment of a subject being considered for immunosuppressive therapy,or a subject with symptoms of meningitis. The method can includedetecting one or more antigens (e.g., one or more polypeptides and/orglycans) of Coccidioides immitis and/or Coccidioides posadasii in a bodyfluid sample from the subject, where the detecting includes lectin-basedand/or antibody-based enrichment of C. immitis and/or C. posadasiiantigens, and detection of one or more of the antigens or theircomponents (e.g., polypeptides or glycans), and stopping or delayingadministration of immunosuppressive therapy. The immunosuppressivetherapy can be for solid organ or hematopoietic stem cell transplant.The immunosuppressive therapy can include administration of one or morecorticosteroids or TNF-alpha inhibitors, one or more glucocorticoids orother immunosuppressive biological agents. In some embodiments, theimmunosuppressive therapy can include administration of cyclosporine,tacrolimus, sirolimus, mycophenolate, muromonab-CD3, antithymocyteglobulin, rituximab, or thalidomide. The method can further includeadministering an anti-fungal agent to the subject. The anti-fungal agentcan include fluconazole, ketoconazole, itraconazole, voriconazole,posaconazole, isavuconazole, or amphotericin. The detecting can includeusing mass spectrometry. The mass spectrometry can generate mass/chargepeaks representing antigens (polypeptides and/or glycans) that areassociated with infection by Coccidioides fungus, or that supply datasuch as sequences or structures of antigens that match Coccidioidesantigens. The mass spectrometry can be MALDI-TOF mass spectrometry orLC-MS/MS. The detecting can include using one or more antibodies againstone or more Coccidioides antigens. The lectin can be sWGA, GSLII, WGA,or a combination of WGA, sWGA, and/or GSLII. The detecting can includeusing one or more lectins that bind to both human and Coccidioidesantigens. The one or more lectins can be Con A, ECL, and PSA. Thedetecting can include using one or more lectins that bind to antigens.The one or more lectins can bind to human antigens and enrichCoccidioides antigens by reducing the number or percentage of humanantigens present in a specimen. In some embodiments, the lectin caninclude one or more of Con A, DSL, ECL, GSLI, JAC, LCA, PNA, PVE, PVL,PSA, RCA I, STL, SBA, UEA I, and VVL. The body fluid sample can includeblood, plasma, serum, urine, saliva, sputum, induced sputum, nasalwashing, bronchial washing, bronchial brushing, tracheal secretions,bronchoalveolar lavage, or cerebrospinal fluid. The volume of the bodyfluid sample can be from 0.02 mL to 200 mL. The body fluid sample can becontacted with the lectin(s) for 1 second to 48 hours.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention pertains. Although methods and materialssimilar or equivalent to those described herein can be used to practicethe invention, suitable methods and materials are described below. Allpublications, patent applications, patents, and other referencesmentioned herein are incorporated by reference in their entirety. Incase of conflict, the present specification, including definitions, willcontrol. In addition, the materials, methods, and examples areillustrative only and not intended to be limiting.

The details of one or more embodiments of the invention are set forth inthe accompanying drawings and the description below. Other features,objects, and advantages of the invention will be apparent from thedescription and drawings, and from the claims.

DESCRIPTION OF DRAWINGS

FIG. 1 includes selected micrographs of infected human lung tissuestained with lectins by immunohistochemistry. Con A: Concanavalin A, GSLII: Griffonia simplicifolia lectin II, PVE=Phaseolus vulgariserythroagglutinin, SWGA=succinylated wheat germ agglutinin. Darker areasindicate reactivity of the lectin with the fungus.

FIG. 2 includes lectin-based IHC micrographs from VF patients.Biotinylated lectins were incubated with infected lung tissues fromseven patients. Darker areas indicate reactivity of lectin. GSLII andsWGA reacted positively and specifically to endospores and spherules,and not to the adjacent human lung tissue.

FIG. 3 contains lectin-based IHC micrographs. Biotinylated lectins wereincubated with infected lung tissues, as indicated. Darker areasindicate reactivity of lectin. Spherules are larger round structureswith or without endospores inside. Arrows indicate examples of spherulesor groups of spherules. GlcNAc-mediated inhibition of sWGA and GSLIIbinding to spherules and endospores is shown at different dilutions.Galactose did not inhibit binding of either lectin to spherules. PVE didnot bind the spherules, but did bind to human lung tissue.

FIGS. 4A and 4B are graphs plotting the binding of GSLII (FIG. 4A) andsWGA (FIG. 4B) to spherules in the presence of decreasing concentrationsof inhibitors, as indicated. Two-fold dilutions of non-biotinylated sWGAand GSLII lectins starting at 20 μM were incubated in an EIA platecoated with Spherulin for 20 minutes. Biotinylated GSLII or sWGA wasadded and incubated for one hour. After washing the plate,streptavidin-HRP was added to detect biotinylated lectins that were notinhibited from binding to Spherulin. After TMB substrate development,the plate was read at 450 nm. The percent of control binding(OD_(biotinylated lectin in with non-biotinylated inhibitor)/OD_(biotinylated lectin without inhibitor)×100)is plotted.

FIGS. 5A and 5B are pictures of SD S-PAGE from GSLII (FIG. 5A) and sWGA(FIG. 5B) lectin columns. Spherulin was used as the starting materialprior to running the column. Washes 1-6 represent six 0.5 ml PBS washescollected from the column (the column bed volume was 0.2 ml). The rightlane in each gel contains eluted glycoproteins that bound to the lectincolumn and were eluted using “Glycoprotein Eluting Solution” (VectorLabs). The GSLII and sWGA elution lanes were sliced and processed fortrypsin digestion and subsequent mass spectrometry analysis.

FIG. 6 is a Venn diagram indicating the total and common proteinsidentified in the GSLII and sWGA lectin column eluates. 145 proteinsbound both lectins; a total of 195 proteins bound to GSLII, and a totalof 224 proteins bound to sWGA. All glycoproteins in the GSLII fractionwere subsets of whole Spherulin and sWGA, and all glycoproteins in thesWGA fraction were subsets of whole Spherulin and GSLII. The proteinsthat were affinity purified on the two lectin columns represent subsetsof the Spherulin proteome.

FIG. 7 is a picture of SDS-PAGE showing that treatment of Spherulin withPNGase (an enzyme that removes N-linked glycan chains from proteins)abrogates the binding of GSLII and sWGA lectins. Lanes are numbered andlabeled according to treatment. Lanes 6 and 8 (boxed) were cut into gelslices, treated with trypsin, and run on an Orbitrap QExactive massspectrometer. Spectra were searched using the Coccidioides posadasii(Silviera strain). Very few spectra were identified, indicating thatlectins were binding glycan on the glycoproteins.

FIG. 8 is a Venn diagram indicating counts of common coccidioidalproteins in patient plasma. Ninety-one proteins and their isoforms(counting proteins represented by two or more tryptic peptides) werecommonly present in plasma acquired from patient 1 and patient 2.

FIG. 9 is Venn diagram of unique glycan precursor m/z values in sixpositive Coccidioidomycosis patients and Coccidioides fungal lysate (CDNAg), that were not identified in the six negative control samples.

FIG. 10 is an example of the glycan structure information derived fromthe precursor m/z value 780.708. All images were acquired in SimGlycan v5.60. FIG. 10A is a diagram indicating M/z versus intensity of parentpeak 780.708 when fragmented into MS/MS spectra. MS/MS spectra thatmatched theoretical glycan fragment masses are shown with theircorresponding sugar structures. FIG. 10B is a diagram generated afterglycan fragments from MS/MS spectra were compiled into a best fit parentglycan molecule. FIG. 10C shows exported results data for the parentscan, showing the retention time that the molecule eluted off thecolumn, its charge state, glycan identification number, theoreticalglycan parent mass, and molecular formula.

DETAILED DESCRIPTION

This document is based, at least in part, on the development ofsensitive and specific methods of detecting VF antigens (e.g., peptidesand/or glycans). In some embodiments, the methods provided herein caninclude contacting a biological sample (e.g., a sample of bodily fluid)from a subject (e.g., a human subject or a non-human mammal such as acanine, feline, rodent, equine, bovine, ovine, or porcine mammal, or amammal in the Delphinoidea superfamily, where the subject has one ormore symptoms of CAP and/or VF) with fixed lectins or antibodies so asto allow purification through a lectin affinity column or lectin-linkedmagnetic particles, for example. Bound VF antigens can be eluted fromthe lectin or antibody and digested with a protease and/or a glycosidaseto generate peptide and/or glycan fragments. The fragments can beanalyzed by, for example, mass spectrometry, to allow specificcharacterization of mass/charge signatures and, in some cases, aminoacid or glycan sequences/structures. In some embodiments, for example, amethod as provided herein can include running a urine sample through asWGA column, eluting the bound antigens (e.g., peptides and/or glycans),and using mass spectrometry to identify specific the antigens. In somecases, the eluted antigens can be digested with trypsin prior to massspectroscopy. Mass spectrometry has a high analytical specificity, asspecific mass/charge peaks typically are highly reproducible andrepresent particular fragments of specific antigens. Thus, theidentification of particular mass/charge signatures that are specific toone or more Coccidioides antigens can be highly predictive of infection.

As described herein, the use of such methods with samples from patientsknown to have active VF resulted in the detection of 91 fungal proteins(see, FIG. 8) and 25 glycans (see, TABLE 1). Thus, the methods providedherein can provide sensitive and specific detection of VF, which canlead to altered or more efficient treatment of affected individuals. Forexample, treatment of patients with antibiotics may be discontinued oncethe patients are affirmatively diagnosed with VF. Not only would such atreatment alteration benefit the patients by targeting the correctpathogen, but also the discontinuation of antibiotic treatment canreduce the risk of C. difficile infection, and also can reduce theoccurrence of antibiotic side effects such as nausea, diarrhea, hearingloss, and risk of tendon rupture. Further, the discontinuation ofunnecessary antibacterial or anti-viral drugs is a broad benefit topublic health, as it lowers the chance of developing resistantorganisms. In addition to Coccidioidomycosis, the methods describedherein may be applicable to the detection of antigens (e.g.,polypeptides and/or glycans) from other pathogens, including fungi suchas, without limitation, Blastomyces sp., Histoplasma sp., Aspergillussp., Candida sp., and Mucor sp.

The methods provided herein can be used to direct treatment decisionsfor patients presenting with, and in some cases undergoing antibacterialor anti-viral treatment for, one or more symptoms of invasive fungalinfection or CAP. Treatment decisions based on the results provided bythis method may include, discontinuation of antibacterial drugs that canbe a risk factor for infection by Clostridium difficile and can causeside effects such as nausea, diarrhea, hearing loss, and tendon rupture.Antibacterial drugs are currently over-utilized, leading to theemergence of resistant organisms. In addition or alternatively,treatment decisions can include the initiation or continuation ofantifungal drugs against Coccidioides, such as fluconazole and/orvoriconazole. In addition, an affirmative diagnosis of VF can allowpractitioners to cease additional testing for other etiologies ofinfection, providing cost-savings for the patient and the health carefacility, and avoiding potential false-positive testing that mightresult in unnecessary treatment.

Thus, in some embodiments, this document provides methods that includedetecting one or more antigens, such as one or more peptides or glycans,or a combination of one or more peptides and one or more glycans, ofCoccidioides immitis and/or Coccidioides posadasii in a biologicalsample from a subject (e.g., a body fluid sample from a subjectexhibiting one or more symptoms of CAP or invasive fungal infection),where the detecting includes (i) lectin-based or antibody-basedenrichment of C. immitis and/or C. posadasii antigens and (ii) detectionof one or more of the antigens or fragments thereof, and stoppingantibacterial or anti-viral treatment if the subject is undergoing suchtreatment, initiating antifungal treatment, or stopping antibacterial oranti-viral treatment and initiating antifungal treatment. Any suitableantifungal treatment that is effective against Coccidioides can be usedto treat a subject diagnosed with VF using the methods described herein.Useful antifungal treatments can include, for example, fluconazole,ketoconazole, itraconazole, voriconazole, posaconazole, isavuconazole,and amphotericin.

This document also provides methods for altering the treatment ofpatients being considered for immune-modifying therapy, or patients withsymptoms of meningitis, where the methods include detecting one or moreC. immitis and/or C. posadasii antigens (e.g., one or more C. immitisand/or C. posadasii polypeptides, glycans, or a combination thereof) ina biological sample from a patient, based on lectin-based orantibody-based enrichment of C. immitis and/or C. posadasii antigens,and detecting one or more of the antigens or components thereof. Thealteration in treatment may include stopping administration ofimmunosuppressive therapy (e.g., immunosuppressive therapy for a solidorgan or stem cell transplant, administration of steroids or TNF-alphainhibitors, administration of a glucocorticoid, administration of tumornecrosis factor alpha (TNF-alpha, or administration of one or more ofcyclosporine, tacrolimus, sirolimus, mycophenolate, muromonab-CD3,antithymocyte globulin, rituximab, or thalidomide), or delayingadministration of such therapy.

As used herein, the term “antigen” can refer to any peptide or glycanfrom a particular organism (e.g., from a fungus of the Coccidioides sp.,Blastomyces sp., Histoplasma sp., Aspergillus sp., Candida sp., or Mucorsp.). As used herein, the term “polypeptide” refers to any chain ofamino acids, regardless of length or post-translational modification(e.g., glycosylation or phosphorylation). A polypeptide can be, forexample, between 5 and 1000 amino acids in length. In some embodiments,a polypeptide is about 10 to about 50 amino acids in length, about 25 toabout 100 amino acids in length, about 50 to about 150 amino acids inlength, about 100 to about 200 amino acids in length, about 200 to about300 amino acids in length, about 300 to about 500 amino acids in length,about 500 to about 750 amino acids in length, or about 750 to about 1000amino acids in length. The term “polypeptide” therefore encompassesrelatively short peptides (e.g., polypeptides that are about 10 to about25 amino acids in length) as well as full length proteins.

As used herein, the term “glycan” refers to any molecule covalentlylinked to one or more monosaccharide molecules, regardless of length ormodification (e.g., acetylation or ionization). A glycan can be, forexample, two or more monosaccharide molecules, one or moremonosaccharide molecules covalently linked to a lipid, one or moremonosaccharide molecules covalently linked to a polypeptide, or one ormore monosaccharide molecules covalently linked to a complex structureof other saccharide units.

Biological samples that can be used in the methods described hereininclude, without limitation, samples of bodily fluid such as blood,plasma, serum, urine, saliva, sputum, induced sputum, nasal washing,bronchial washing, bronchial brushing, tracheal secretions,bronchoalveolar lavage, and cerebrospinal fluid. The volume of abiological sample can range from about 0.02 mL to about 200 mL, or anyamount or range there between (e.g., about 0.02 mL to about 0.5 mL,about 0.5 mL to about 1 mL, about 1 mL to about 3 mL, about 3 mL toabout 10 mL, about 10 mL to about 100 mL, or about 100 mL to about 200mL).

The biological sample can be contacted with one or more immobilizedlectins or antibodies (e.g., on a lectin affinity column orlectin-linked magnetic particles), in order to enrich or purifyCoccidioides antigens (e.g., peptides and/or glycans) that may be in thebiological sample. In some embodiments, the biological sample can beincubated with one or more lectins for up to 48 hours (e.g., from about1 second to about 48 hours, about 1 second to about 60 seconds, about 1minute to about 5 minutes, about 5 minutes to about 10 minutes, about 10minutes to about 30 minutes, about 30 minutes to about 60 minutes, about1 hour to about 3 hours, about 3 hours to about 6 hours, about 6 hoursto about 12 hours, about 12 hours to about 24 hours, or about 24 hoursto about 48 hours).

The one or more lectins with which the biological sample is contactedcan include one or more (e.g., one, two, three, four, five, two or more,three or more, four or more, or five or more) of the following: wheatgerm agglutinin (WGA), succinylated WGA (sWGA), Griffonia simplicifoliaII lectin (GSLII), Concanavalin A (Con A), Erythrina crystagalli Lectin(ECL), and Pisum sativum Agglutinin (PSA). In some embodiments, one ormore lectins selected from Con A, Datura stramonium lectin (DSL), ECL,Griffonia simplicifolia lectin I (GSLI), Jacalin (JAC), Len culinarislectin (LCA), peanut agglutinin (PNA), Phaseolus vulgariserythroagglutinin (PVE), Phaseolus vulgaris leukoagglutinin (PVL), PSA,Ricinus communis agglutinin (RCA I), Solanum tuberosum lectin (STL),soybean agglutinin (SBA), Ulex europaeus agglutinin I (UEA I), and Viciavillosa lectin (VVL) may bind to human glycans in the biological sample,thus enriching Coccidioides polypeptides by reducing the number orpercentage of free human glycoproteins or free glycans present in thebiological sample.

Coccidioides antigens can be detected using any suitable method. Massspectrometry can be particularly useful, however. As noted above, massspectrometry has a high analytical specificity since specificmass/charge peaks typically are highly reproducible. Thus, massspectrometry can be used to generate mass/charge peaks representative ofantigens from the Coccidioides fungus. In some embodiments, matrixassociated laser desorption ionization time of flight (MALDI-TOF) massspectrometry or liquid chromatography followed by tandem massspectrometry (LC-MS/MS) can be used.

It is to be noted that this document also contemplates detection anddiagnosis of conditions associated with other types of fungi, such asBlastomyces sp., Histoplasma sp., Aspergillus sp., Candida sp., andMucor sp., for example. Thus, using a lectin column and doing a glycanextraction by mass spectroscopy as described herein for Coccidioides,biomarkers as defined by certain mass/charge peaks specific for othergenera of fungi (e.g., Histoplasma and Blastomyces) can be detected, andsubjects can be diagnosed and treated effectively.

The invention will be further described in the following examples, whichdo not limit the scope of the invention described in the claims.

EXAMPLES Example 1—Lectin Reactivity to Coccidioides in Infected LungTissue and Demonstration of GSLII and sWGA Binding to CoccidioidalProteins Methods

Lectin-Based Immunohistochemistry (IHC): IHC was performed usingformalin-fixed paraffin embedded (FFPE) blocks obtained from patientswith VF. Five (5) μm tissue sections from seven patients who underwenteither lobectomy, wedge resection, or excisional biopsy from a skinlesion (wrist) were used for IHC. Tissue sections on slides were blockedin Alkaline Phosphatase/Horseradish Peroxidase Block (SurModics, Cat#APHP-0111-01) for 15 minutes, followed by Carbo-Free Blocking Solution(Vector Laboratories, Cat# SP-5040) for 1 hour. Biotinylated lectinswere obtained from Vector Laboratories (Cat# B-1215, B-10255).Preliminary experiments were performed to optimize the lowestconcentration of lectin that showed positive staining, which was 2 μg/mlfor both GSLII and sWGA. Biotinylated lectins bound to tissue sectionswere detected with streptavidin (SA) coupled to horseradish peroxidase(HRP) using Diaminobenzidine (DAB) as substrate. Sections were washedwith 1×PBS (3 times for 5 minutes each) between blocking, incubationwith lectin, detection with SA-HRP, and staining with DAB. Tissue wascounterstained using hematoxylin (Santa Cruz Cat# SC-24973). GSLII andsWGA were inhibited with serial dilutions of chitin hydrolysate, aconcentrated solution of GlcNAc (Vector Labs, Cat# SP-0090). Phaseolusvulgaris erythrolectin (PVE), a lectin that binds Galβ4GlcNAcβ2Manα6,was used as a negative lectin control.

Inhibition of Lectin-Based IHC: To support the hypothesis of lectin-likebinding to spherules and endospores, reactivity of GSLII and sWGA wasinhibited in a concentration-dependent manner with commercial solutionof monomeric and oligomeric GlcNAc (100 mM). A high concentration ofGlcNAc (1:4 dilution; 25 mM) was required to completely inhibit sWGAbinding to the spherules, while a relatively lower amount of GlcNAc(1:400 dilution; 0.25 mM) inhibited GSLII binding, suggesting that sWGAbinding to spherules and endospores is stronger than GSLII (FIG. 3).When galactose (non-specific sugar) was used to inhibit the binding ofthese two lectins to the fungal spherules, there was a complete lack ofinhibition.

Lectin-Based Inhibition EIA: Spherulin was coated onto a flat-bottom 96well microtiter plate at 1 μg/ml in PBS for one hour at roomtemperature. Wells were blocked with 1% carbo-free BSA in PBS for anadditional hour. Two-fold (starting from 1 μM) dilutions ofnon-biotinylated sWGA and GSLII were used to challenge the binding ofbiotinylated GSLII and sWGA, respectively. For instance,non-biotinylated sWGA was incubated with biotinylated GSLII for 10minutes prior to placement on the plate. Non-biotinylated lectindilutions started at 1 μM, and biotinylated lectins were held constantat 10 nM. The mixture was then added to the plate for one hour. PVE wasused as a negative lectin control. Bound lectins were detected with a5000-fold dilution of SA-HRP (Thermo-Pierce, Cat #21130) in PBS. Plateswere washed three times with PBS containing 0.05% Tween-20 (PBST)between coating, blocking, incubation with lectin, detection withSA-HRP, and addition of 3, 3′, 5, 5′-Tetramethylbenzidine (TMB)(Becton-Dickinson, Cat#555214). 1N H₂SO₄ was used to stop the HRPenzyme, and the plate was read in a Molecular Diagnostics plate readerat 450 nm using SoftmaxPro software. The percent of control wascalculated using the following formula:(OD_(biotinylated lectin in presence of non-biotinylated inhibitor))/(OD_(biotinylated lectin in the absence of inhibitor))×100=percentof control.

Results

Twenty-one lectins were tested for their reactivity to Coccidioidesspherules and endospores in infected human lung tissue, usinglectin-based immunohistochemistry (IHC). Coccidioides-binding lectinsidentified in these studies were confirmed and tested for their abilityto bind to laboratory-grown Coccidioides using a lectin-basedenzyme-linked immunosorbent assay (EIA). Known binding properties (sugarspecificities) of Coccidioides-binding lectins were then confirmed usingboth IHC and EIA inhibition assays.

The lectins tested for binding to Coccidioides spherules are listed inTABLE 1. Representative micrographs indicating binding patterns forcertain lectins (Con A, GSLII, PVE, and sWGA) are shown in FIG. 1. Twoof these (GSLII and sWGA) exhibited specific staining of spherules andendospores, and did not bind to adjacent lung tissue. Other lectins,such as PVE, bound to lung tissue but not to spherules and endospores,while ConA, in particular, bound spherules, endospores and adjacenttissue. The binding properties of GSLII and sWGA was confirmed withseven patients, showing the specific binding to Coccidioides was commonamong different individual patients' coccidioidal infections anddifferent and tissues (FIG. 2).

Both GSLII and sWGA have known specificity for GlcNAc. When theselectins were pre-incubated with chitin hydrolysate (GlcNAc) prior toaddition to infected lung tissue, binding of both sWGA and GSLII tospherules and endospores was inhibited (FIG. 3). These experimentsindicated that sWGA and GSLII interact with GlcNAc groups on fungalproteins. Galactose did not inhibit binding.

To confirm the lectin-based IHC results and assess whether sWGA andGSLII compete for the same glycan structure, an inhibition EIA wasperformed on Spherulin coated plates using biotin-GSLII and biotin-sWGAas detection agents. As shown in FIGS. 4A and 4B, sWGA inhibits bindingof biotinylated GSLII to Spherulin in a concentration-dependent manner,with a relative IC50 of 1.5 μM. In contrast, 50% inhibition of 1 nMbiotinylated sWGA was not reached with GSLII, even at 20 μM, suggestinghigher avidity of sWGA for GlcNAc on coccidioidal glycoproteins thanGSLII. PVE, a Galβ4GlcNAcβ2Manα6 binding lectin, did not inhibit eitherGSLII or sWGA, and served as a “control” lectin.

Taken together, these studies identified lectins that bind specificallyto Coccidioides spherules and endospores in infected humans, and showedin particular that GSLII and sWGA, two GlcNAc-binding lectins, bindspecifically to coccidioidal glycoproteins in spherules and endosporespresent in infected human lung tissue, and bind specifically to proteinsin laboratory grown Coccidioides spherules. Interestingly, only two ofthe five GlcNAc-binding lectins tested (GSLII, sWGA, DSL, LEL, and STL)bound specifically to spherules and endospores in lung tissue,suggesting that the affinity-purified glycoproteins have terminalGlcNAcs or specific glycan linkages that may be involved in theirbinding specificities. The most abundant lectin affinity-purifiedglycoproteins from Coccidioides are involved in growth and metabolism ofthe fungus.

TABLE 1 Lectins tested, their known sugar specificities, and theirreactivity in infected human lung tissue. Bolded lectins exhibitedspecific staining of spherules and endospores. Reactivity in InfectedLectin Sugar Specificity Lung Tissue Concanavalin A (Con A) MannoseSpherules, endospores, and lung tissue Datura stramonium LectinN-Acetylglucosamine, Lung tissue (DSL) Dolichos biflorus AgglutininN-Acetylgalactosamine No reactivity (DBA) Erythrina crystagalli LectinGalactose Spherules and lung (ECL) tissue (some reactivity) Griffoniasimplicifolia Galactose Not fully characterized Lectin I (GSL I)

N-Acetylglucosamine Spherules and Lectin I (GSL II) (GlcNAc) endosporesJacalin Galactose Lung tissue Len culinaris Lectin (LCA) Mannose Lungtissue (some reactivity) Lycopersicon esculentum N-Acetylglucosamine Noreactivity Lectin (LEL) Peanut Agglutinin (PNA) Galactose Lung tissue(some reactivity) Phaseolus vulgaris Complex N-glycans Lung tissueErythroagglutinin (PVE) Phaseolus vulgaris Complex N-glycans Lung tissueLeukoagglutinin (PVL) Pisum sativum Agglutinin Mannose Spherules,endospores, (PSA) and lung tissue Ricinus communis Galactose, N- Lungtissue Agglutinin I (RCA I) Acetylglucosamine Solanum tuberosum LectinN-Acetylglucosamine Lung tissue (some (STL) reactivity) Sophora japonicaN-Acetylgalactosamine No reactivity Agglutinin (SJA) Soybean Agglutinin(SBA) N-Acetylgalactosamine Lung tissue (some reactivity) SuccinylatedWheat Germ N-Acetylglucosamine Spherules and Agglutinin (sWGA) (GlcNAc)endospores Ulex europaeus Agglutinin I Fucose Lung tissue (some (UEA I)reactivity) Vicia villosa Lectin (VVL) N-Acetylgalactosamine Lung tissue(some reactivity) Wheat Germ Agglutinin N-Acetylglucosamine Spherulesand (WGA) endospores

Example 2—Spherulin Proteome and Lectin-Binding Glycoproteome of C.Posadasii Methods

Preparation of Spherulin: C. posadasii (strain Silvera) spherule-phasecells were maintained in continuous culture at 40° C., 20% CO₂, withcontinuous shaking at 120 RPM in modified Converse medium (Cox andBritt, Infect Immun 55(11):2590-2596, 1987). In brief, cultures wereinitiated by seeding flasks of Converse medium with ˜1-5×10⁵arthrospores/ml. At three to four day intervals, the cells collected bycentrifugation, washed in sterile distilled water, and stored at 4° C.in 0.5% formalin in water. Prior to fixing in formalin, the cells werechecked by microscopy to ensure that the culture was mixed-phasespherules and endospores by morphology and for purity by culture onglucose-yeast extract agar plates. The spent medium was supplemented to0.5% formalin and stored at 4° C. The spent medium contained antigenselaborated during cellular growth (Spherulin filtrate, SPH-F). The SPH-Fantigens were concentrated using a 10,000 MW ultrafiltration membrane.The collected mixed-phase spherules and endospores were processed toobtain the lysate antigen preparation (Spherulin lysate, SPH-L). Torelease the internal antigens, the fungal cells were processed in anice-cooled Beadbeater using 0.5 mm glass beads for 5 minutes. Cellulardebris was removed by centrifugation (6,000×g, 10 minutes) and thesupernatant collected. Both SPH-F and SPH-L were lyophilized and storedat −80° C. until use. SPH-L and SPH-F were combined in these studies,and are referred to as “Spherulin.”

Spherulin analysis using LC-MS/MS: 20 μs of Spherulin was suspended inSDS sample loading buffer (50 mM Tris-HCl, pH 6.8, 2% SDS, 10% glycerol,1% 2-mercaptoethanol, 12.5 mM EDTA and 0.02% bromophenol blue) andheated to 95° C. The proteins were then separated by 12% SDS-PAGE andstained with Bio-Safe Coomassie G-250 Stain. Each lane of the SDS-PAGEgel was cut into six equal size slices, placed in a 0.6-ml polypropylenetube, destained twice with 375 μl of 50% acetonitrile (ACN) in 40 mMNH₄HCO₃, and dehydrated with 100% ACN for 10 minutes. After removal ofACN by aspiration, the gel pieces were dried in a vacuum centrifuge at60° C. for 30 minutes. Trypsin (250 ng; Sigma) in 20 μl of 40 mM NH₄HCO₃was added, and the samples were maintained at 4° C. for 15 minutes priorto the addition of 50 μl of 40 mM NH₄HCO₃. Digestion was allowed toproceed at 37° C. overnight and was terminated by addition of 10 μl of5% formic acid (FA). After further incubation at 37° C. for 30 minutesand centrifugation for 1 minute, each supernatant was transferred to aclean polypropylene tube. The extraction procedure was repeated using 40μl of 0.5% FA, and the two extracts were combined. The resulting peptidemixtures were purified by solid phase extraction (C18 ZipTip) aftersample loading in 0.05% heptafluorobutyric acid:5% FA (v/v) and elutionwith 4 μl of 50% ACN:1% FA (v/v) and 4 μl of 80% ACN:1% FA (v/v),respectively. The eluates were combined and dried by vacuumcentrifugation, and 6 μl of 0.1% FA (v/v) was added, followed bysonication for 2 minutes. The sonicated samples were brieflycentrifuged, and 2 μl of the sample was subsequently analyzed by massspectrometry as described below.

Lectin Affinity Chromatography: GSLII and sWGA coupled to agarose beadswere purchased from Vector Labs (Cat# AL1213 and AL1023S) and used toaffinity-purify glycoproteins from Spherulin. 500 μg of Spherulindissolved in PBS was applied to lectin-agarose columns (0.5 ml bedvolume). Spherulin starting material and column flow through were savedfor subsequent SDS-PAGE analysis. Ten bed volumes of PBS were used towash the column of unbound lysate. The last 200 ul of PBS wash was savedfor mass spec analysis to ensure that glycoproteins were notnon-specifically washing off the column. Then three bed volumes of“Glycoprotein Eluting Solution for GlcNAc Binding Lectins” (Vector Labs,Cat# ES5100) were used to elute glycoproteins bound to GSLII andsWGA-Agarose. The elutions were collected, and concentrated byultrafiltration to 50 μl using Amicon Ultra 0.5 ml 3 KDa cutoffcentrifugal filters (Cat # UFC500396). Protein content in theconcentrated eluates were measured using the Micro BCA Protein Assay Kit(Thermo Pierce, Cat#23235) according to the manufacturer's directions.

Deglycosylation: Spherulin was deglycosylated using a PNGaseF kitaccording to the manufacturer's instructions (New England Biolabs, Cat#P0704L). Briefly, 500 μg of Spherulin was denatured using 10×glycoprotein denaturation buffer at 95° C. for 5 minutes, followed by 5minutes on ice. For deglycosylation, 10× G7 Reaction Buffer, 10% NP40,and PNGase were added and allowed to incubate for 6 hours at 37° C.Deglycosylated Spherulin was applied to lectin bound agarose beads incolumns (as above), and eluates were analyzed by SDS-PAGE and digestedwith trypsin. SDS-PAGE gel bands were prepared for mass spectrometryanalysis using the following procedures. Colloidal blue stained gelbands were destained in 50% acetonitrile/50 mM Tris pH 8.1 until clear,and the proteins were reduced with 50 mM TCEP/50 mM Tris pH 8.1 at 55°C. for 30 minutes, followed with alkylation using 20 mM iodoacetamide/50mM Tris pH 8.1 at room temperature for 30 minutes in the dark. Proteinswere digested in situ with 0.15 μg trypsin (Promega Corporation,Madison, Wis.) in 25 mM Tris pH 8.1/0.0002% Zwittergent 3-16, at 37° C.overnight, followed by peptide extraction with 2% trifluoroacetic acidand acetonitrile. The pooled extracts were concentrated and the proteinswere identified by nano-flow liquid chromatography electrospray tandemmass spectrometry (nanoLC-ESI-MS/MS) using a Thermo ScientificQ-EXACTIVE PLUS™ Mass Spectrometer (Thermo Fisher Scientific; Bremen,Germany) coupled to a Thermo ULTIMATE™ 3000 RSLCnano HPLC system.

Mass Spectrometry: Peptides present in each sample were loaded onto a0.25 μL bed OPTIPAK® trap (Optimize Technologies; Oregon City, Oreg.)custom-packed with 5 μm, 200 A Magic C18 stationary phase. The loadedtrap was washed for 4 minutes with an aqueous loading buffer of 0.2% FAand 0.05% TFA at 10 μL/minute. Following the wash, peptides weretransferred onto a 35 cm×100 μm PICOFRIT® column, self-packed withAgilent Poroshell 120S 2.7 μm EC-C18 stationary phase, using a DionexULTIMATE® 3000 RSLC liquid chromatography (LC) system (Thermo; San Jose,Calif.). Peptides were separated using a 400 nL/minute LC gradientcomprised of 2%-40% B in 0-70 minutes. Mobile phase A was 2%acetonitrile (ACN) in water with 0.2% FA, and mobile phase B wasACN/isopropanol/water (80/10/10 by volume) with 0.2% FA. Elutingpeptides were analyzed using a Q-EXACTIVE PLUS™ mass spectrometer(Thermo-Fisher, Waltham, Mass.). The instrument was configured tooperate in data-dependent mode by collecting MS1 data at 70,000resolving power (measured at m/z 200) with an AGC value of 1E6 over am/z range of 360-2000, using lock masses from background polysiloxanesat m/z 371.10123 and 446.12002. Precursors were fragmented withnormalized collision energy (NCE) of 28, fragments measured at 17,500resolving power and a fixed first mass of 140. Resulting tandem massspectra (MS/MS) were collected on the top 20 precursor masses present ineach MS1 using an AGC value of 1E5, max ion fill time of 50 ms, and anisolation window of 1.5 Da. All raw data files were transcoded into mzMLformat using msConvert tool of the ProteoWizard library (PMID:18606607).

Bioinformatics: A composite protein sequence database was compiled toidentify the Coccidioides proteins present in the lysate. This databasecontained Coccidioides proteomes obtained from the Broad Institute'sCoccidioides Genomes project (Neafsey et al., Genome Res 20(7):938-946,2010; and Sharpton et al., Genome Res 19(10):1722-1731, 2009), SwissProtand RefSeq. RefSeq human and bovine proteomes were added to thisdatabase to prevent misidentification of proteins originating from cellculture and other human contamination as Coccidioides proteins. Commoncontaminants (wool, cotton, etc.) were added to the database to accountfor sample handling artifacts. Reversed protein sequences were appendedto the database to estimate protein and peptide identification falsediscovery rates (FDRs).

The MyriMatch (Tabb et al., J Proteome Res 6(2):654-661, 2007) (version2.1.38) database search engine was used to match the MS/MS present ineach data file against the composite protein sequence database. Thesoftware was configured to use 10 ppm m/z tolerance for both precursorsand fragments while performing peptide-spectrum matching. The softwarederived semitryptic peptides from the sequence database while lookingfor the following variable modifications: carbamidomethylation ofcysteine (+57.023 Da.), oxidation of methionine (+15.994 Da.), andformation of N-terminal pyroglutamic acid (−17.023 Da.). IDPicker(version 3.0.504) software filtered the peptide-spectrum matches at 2%FDR. The software was configured to use an optimal combination of MVH,mzFidelity and XCorr scores for filtering. Protein identifications withat least two unique peptide identifications were considered to bepresent in the sample. Resulting proteins were clustered into groups ofproteins that match the same set of peptides.

Results

Mass Spectrometric Identification of Proteins in UnfractionatedSpherulin: Given the results from the IHC and EIA using Spherulin asantigen, the first step in the lectin-binding proteomic analysis ofCoccidioides was to identify the complete proteome of Spherulin. Threedifferent Coccidioides databases (SwissProt, RefSeq, and BroadInstitute's Coccidioides Genomes project (Neafsey et al., supra; andSchiess et al., Mol Oncol 3(1):33-44, 2009) were employed to search theMS/MS spectra derived from Spherulin. A total of 1390 proteins wereidentified in Spherulin. A listing of the ten most abundant coccidioidalproteins in Spherulin with high tryptic fragment coverage is shown inTABLE 2. All of these proteins have an effective FDR of 0.0%. Eight ofthe top ten identified proteins in Spherulin are metabolic enzymesimportant for fungal growth. The second most abundant Spherulin proteinidentified is a “conserved hypothetical protein” (CPSG_03975) with apentapeptide (PT) repeat sequence, and has high homology with anexoprotein involved in adhesion. This finding indicated that CPSG_03975is no longer “hypothetical” and is highly abundant during fungal growthin vitro. In total, 434 hypothetical proteins were identified,constituting 31% of the total proteins entries in the proteome ofSpherulin.

Other highly abundant proteins found in Spherulin were5-methyltetra-hydropteroyltriglutamate-homocysteine methyltransferase(MET-E; CPSG_03208), Heat shock protein 90 (CPAG_06539),3-isopropylmalate dehydrogenase (CPAG_08709), glucose-6-phosphateisomerase (CPAG_05681), enolase (CPAG_04681) and fructose biphosphatealdolase (CPAG_09270).

SDS-PAGE and Identification of Proteins from GSLII and sWGA AffinityPurified Spherulin Eluates: GSLII and sWGA lectins bind to spherules andendospores in infected human lung tissue sections. Since the principlecomponent of chitin is GlcNAc, it was possible that the lectins simplybound to chitin. However, it also was possible that GlcNAc structuresare present on coccidioidal glycoproteins and are accessible to thelectins. Lectin-affinity chromatography of Spherulin, followed bySDS-PAGE, was conducted to determine if there were any glycoproteinsthat bound to GSLII and sWGA lectins. After Spherulin was loaded ontoGSLII and sWGA columns, they were washed extensively and eluted with“Glycoprotein Eluting Solution.” The eluted material was dialyzed,concentrated and quantified as described above. FIGS. 5A and 5B showSDS-PAGE gels of Spherulin elution profiles from GSLII and sWGA columns,respectively. Mass spectrometric analysis of Wash 6 (FIGS. 5A and 5B)from the GSLII and sWGA columns did not reveal any coccidioidalproteins, indicating that the remaining material bound to the lectincolumns was specific for lectin.

To identify the lectin-binding glycoproteins in Spherulin, thelectin-chromatography enriched glycoproteins were identified usingtandem mass spectrometry and analysis of MS/MS spectra. In addition, ananalysis was conducted to determine if the enrichment by lectinchromatography enabled detection of additional glycoproteins notidentified in whole Spherulin. Searching spectra from tryptic peptidesagainst the C. posadasii (strain Silviera) databases (The BroadInstitute's Coccidioides Genomes project, RefSeq, and SwissProt)revealed that 195 coccidioidal glycoproteins bound to GSLII (FDR of1.11%), while 224 glycoproteins bound to sWGA (FDR of 1.01%). A total of145 fungal glycoproteins bound to both GSLII and sWGA lectins (FIG. 6).The ten most abundant coccidioidal glycoproteins eluted from both theGSLII and sWGA lectin columns (highest tryptic peptide coverage) arelisted in TABLE 3. The table also lists the percentage peptide coveragefor these proteins as well as the unique peptide count for each of thereplicate runs from GSLII and sWGA columns. Many hypothetical proteinsalso were identified in the lectin affinity analysis (36 in the GSLIIanalysis and 54 in the sWGA analysis). A highly abundant hypotheticalprotein (CPSG_01012), different from the hypothetical protein identifiedin whole Spherulin (see below), bound to both lectins. This hypotheticalprotein has 70% sequence similarity to a ribonuclear protein bindingdomain protein from Aspergillus and other fungi. Other abundantglycoproteins in the lectin analysis included5-methyltetrahydropteroyl-triglutamate-homocysteine methyltransferase(CPSG_03208), malate dehydrogenase (CPAG_07192), glucose-6-phosphateisomerase (CPAG_05681, and complement fixation-chitinase (CPSG_08657).The lectin-binding glycoproteome constitutes a subset of the proteomederived from Spherulin (FIG. 6).

To further support the evidence that the binding of the lectins was dueto GlcNAc structures on proteins, Spherulin was deglycosylated withPNGase F, which cleaves glycans from proteins at asparagine residues(except when there is an α1-3 fucose on the core GlcNAc of theglycoprotein). Deglycosylated Spherulin was run through both GSLII andsWGA columns, followed by SDS-PAGE and trypsin digestion using themethods described above. Mass spectrometry analysis of thePNGase-treated elutions from GSLII and sWGA lectin columns demonstratednearly complete loss of binding by deglycosylated coccidioidalglycoproteins to the lectin columns (TABLE 3 and FIG. 7). This suggestedthat the binding of coccidioidal glycoproteins is lectin-like andspecific for GlcNAc. Once the glycoproteins were deglycosylated, they nolonger bound to the lectin chromatography columns (the eluate profile ofdeglycosylated Spherulin for sWGA and GSLII affinity columns is shown inlanes 6 and 8, respectively, of FIG. 7).

TABLE 2 Mass spectrometric identification of the top ten coccidioidalproteins in Spherulin (i.e., the ten with the highest number of trypticpeptides). % Unique tryptic sequence peptides identified Protein IDcoverage from Spherulin5-methyltetrahydropteroyltriglutamate-homocysteine 89 188methyltransferase (CPSG_03208) conserved hypothetical protein(CPSG_03975) 86 89 3-isopropylmalate dehydrogenase (CPAG_08709) 91 89malate dehydrogenase (CPAG_07192) 89 89 heat shock protein 90(CPAG_06539) 78 87 enolase (CPAG_04681) 77 86 fructose biphosphatealdolase (CPAG_09270) 79 78 H538.4 glucose-6-phosphate isomerase(CPAG_05681) 80 78 malate synthase (CPAG_07630) 71 73 fumarate reductaseOsm1 (CPSG_05536) 83 70

TABLE 3 Mass spectrometric identification of top ten coccidioidalglycoproteins in Spherulin that bound to both GSLII and sWGA lectins.CPAG and CPSG numbers denote accession numbers. The number of trypticpeptides in each of three technical replicates for each glycoprotein isshown. “PNGase GSLII” and “PNGase sWGA” indicate that Spherulin wasdeglycosylated with PNGase prior to lectin affinity chromatography.Unique peptides Unique peptides Unique peptides Unique peptides *Max %in GLSII in sWGA in PNGase in PNGase sequence replicates replicatesGSLII replicates sWGA replicates Protein ID coverage 1 2 3 1 2 3 1 2 1 25-methyltetrahydropteroyl- 89 23 16 19 28 15 20 0 0 0 0triglutamate-homocysteine methyltransferase (CPSG_03208) malatedehydrogenase 89 13 7 10 25 11 11 0 0 0 0 (CPAG_07192) fructosebiphosphate 78 12 7 7 15 8 10 0 0 0 0 aldolase (CPAG_09270) enolase(CPAG_04681) 77 13 9 9 9 8 10 0 0 1 0 3-isopropylmalate 91 13 6 7 12 8 90 0 0 0 dehydrogenase (CPAG_08709) glucose-6-phosphate 76 12 0 5 14 2 30 0 0 0 isomerase (CPAG_05681) aldehyde reductase 1 68 12 4 6 12 5 6 0 00 0 (CPAG_06394) hypothetical protein 60 13 10 8 5 2 10 0 0 0 0(CPSG_01012) heat shock protein 90 62 12 5 2 8 6 8 0 0 0 0 (CPAG_06539)complement fixation- 75 10 5 4 20 8 9 0 0 0 0 chitinase (CPSG_08657)*Maximum % sequence coverage from all replicates.

Example 3—Proteomic Analysis of Coccidioides Infected Human Lung Tissue,Urine and Plasma with Mass Spectrometry Methods

Collection of Patient Plasma, and Urine: Plasma samples were collectedfrom five VF patients, and control plasma was obtained from threehealthy blood donors from a non-endemic region (Rochester, Minn.). Thefive VF patients were all definitively diagnosed withcoccidioidomycosis. Clinical information for the patients follows.

Patient 1: Long term history of VF was reported. At the time of plasmacollection for this study, leg lesion and urine cultures grewCoccidioides. Serology tests around the time of sample collection alsoconfirmed the diagnosis: CF test was positive with titer of 1:32, IgGpositive by ID and EIA. The patient also suffered from rheumatoidarthritis and was on immunosuppressive agents (leflunomide andprednisone).

Patient 2: Patient was diagnosed with disseminated coccidioidomycosiswith meningitis, miliary pneumonia, and dissemination to bone at thetime of sample collection.

Patient 3: Presented with fatigue, malaise, drenching sweats,non-productive cough, weight loss and dull headache. Left lower lobe oflung showed 2×2 cm nodule and other nodules <4 mm. Diagnostic testresults as follows—CSF serology=1:2 CF, EIA positive for both IgM andIgG, ID negative.

Patient 4: Patient was diagnosed with peritoneal coccidioidomycosis.Diagnosis was confirmed with serology testing (CF titer at 1:64 at thetime of sample collection).

Patient 5: Patient presented with a chronic cough and fatigue with lowgrade fever. Serologic tests were positive at the time of plasma samplecollection (CF titer of 1:32, EIA positive), and findings on chestradiography were consistent with a diagnosis of pulmonarycoccidioidomycosis.

Urine samples were collected from Patient 1 and a normal volunteer donor(control urine).

Lectin Affinity Chromatography with Plasma and Urine: Fifty (50) μl ofplasma was ultra-filtered with a 30 kD filter (Millipore, USA) andfiltrate was collected. Gravity packed sWGA lectin columns were madewith 400 μl slurry. The filtered plasma was diluted with 450 μl of 1×PBSand allowed to bind to the lectin agarose beads for an hour at roomtemperature with end-on-end shaking. The column was then drained andwashed with 5-bed volumes of 1×PBS. Glycoproteins were eluted using anN-acetyl-glucosamine elution buffer (Vector Labs). The eluate wasdialyzed and concentrated against 1×PBS using a 3 kD ultra filter.

Five hundred (500) μl urine was centrifuged at 10,000 rpm, andsupernatant was collected and filtered with a 0.22 μm filter. Thefiltered supernatant was then diluted with 1×PBS and applied to a sWGAlectin column as described above.

SDS-PAGE and in-Gel Trypsin Digestion: SD S-PAGE was performed on lectinenriched samples and bands were prepared for mass spectrometry analysisusing the following procedures. Colloidal blue stained gel bands weredestained in 50% acetonitrile/50 mM Tris pH 8.1 until clear, and theproteins were reduced with 50 mM TCEP/50 mM Tris pH 8.1 at 55° C. for 30minutes, followed with alkylation using 20 mM iodoacetamide/50 mM TrispH 8.1 at room temperature for 30 minutes in the dark. Proteins weredigested in situ with 0.15 μg trypsin (Promega Corporation; MadisonWis.) in 25 mM Tris pH 8.1/0.0002% Zwittergent 3-16, at 37° C.overnight, followed by peptide extraction with 2% trifluoroacetic acidand acetonitrile. The pooled extracts were concentrated and the proteinswere identified by nano-flow liquid chromatography electrospray tandemmass spectrometry (nanoLC-ESI-MS/MS) using a Thermo ScientificQ-Exactive Plus Mass Spectrometer (Thermo Fisher Scientific) coupled toa Thermo Ultimate 3000 RSLCnano HPLC system.

Mass Spectrometry: Tryptic peptides present in each sample were loadedonto a 0.25 μL bed OPTIPAK® trap (Optimize Technologies) custom-packedwith 5 μm of 200A Magic C18 stationary phase. The loaded trap was washedfor 4 minutes with an aqueous loading buffer of 0.2% FA and 0.05% TFA at10 μL/minute. Following the wash, peptides were transferred onto a 35cm×100 μm PICOFRIT® column, self-packed with Agilent Poroshell 120S 2.7um EC-C18 stationary phase, using a Dionex ULTIMATE® 3000 RSLC liquidchromatography (LC) system (Thermo). Peptides were separated using a 400nL/minute LC gradient comprised of 2%-40% B in 0-70 minutes. Mobilephase A was 2% acetonitrile (ACN) in water with 0.2% FA, and mobilephase B was ACN/isopropanol/water (80/10/10 by volume) with 0.2% FA.Eluted peptides were analyzed using a QExactive Plus mass spectrometer(Thermo-Fisher). The instrument was configured to operate indata-dependent mode by collecting MS1 data at 70,000 resolving power(measured at m/z 200) with an AGC value of 1E6 over a m/z range of360-2000, using lock masses from background polysiloxanes at m/z371.10123 and 446.12002. Precursors were fragmented with normalizedcollision energy (NCE) of 28, fragments measured at 17,500 resolvingpower and a fixed first mass of 140. Resulting tandem mass spectra(MS/MS) were collected on the top 20 precursor masses present in eachMS1 using an AGC value of 1E5, max ion fill time of 50 ms, and anisolation window of 1.5 Da. All raw data files were transcoded into mzMLformat using msConvert tool of the ProteoWizard library (Kessner et al.,Bioinformatics 24(21):2534-2536, 2008).

Bioinformatics: A composite protein sequence database was compiled toidentify the Coccidioides proteins present in the lysate. This databasecontained Coccidioides proteomes obtained from the Broad Institute'sCoccidioides Genomes project, SwissProt and RefSeq (Neafsey et al.,supra; and Sharpton et al., supra). RefSeq human and bovine proteomeswere added to this database to prevent misidentification of proteinsoriginating from cell culture and other human contamination asCoccidioides proteins. Common contaminants (wool, cotton, etc.) wereadded to the database to account for sample handling artifacts. Reversedprotein sequences were appended to the database to estimate protein andpeptide identification false discovery rates (FDRs).

MyriMatch (version 2.1.38) database search engine matched the MS/MSpresent in each data file against the composite protein sequencedatabase (Tabb et al., supra). The software was configured to use 10 ppmm/z tolerance for both precursors and fragments while performingpeptide-spectrum matching. The software-derived semitryptic peptidesfrom the sequence database while looking for the following variablemodifications: carbamidomethylation of cysteine (+57.023 Da.), oxidationof methionine (+15.994 Da.) and formation of n-terminal pyroglutamicacid (−17.023 Da.). IDPicker (version 3.0.504) software filtered thepeptide-spectrum matches at 2% FDR (Kessner et al., supra; and Ma etal., J Proteome Res 8(8):3872-3881, 2009). The software was configuredto use an optimal combination of MVH, mzFidelity and XCorr scores forfiltering. Identified proteins with at least two unique peptideidentifications were considered to be present in the sample. Theresulting proteins were clustered into groups that matched the same setof peptides.

Results

Coccidioides Proteins in Patient Plasma: Both GSLII and sWGA were usedin the initial experiments. After 30 kD ultrafiltration and sWGA lectinchromatography, 150 proteins were identified in Patient 1 with trypticpeptides equal to or greater than 1. Among these, at least 2 peptideswere identified for 125 different proteins (the number of trypticfragments per protein ranged from 2 to 26). Using sWGA affinitychromatography enrichment, 125 proteins were identified with 2 or morepeptides, and 24 proteins were identified with a single peptide (total149 proteins).

Patient 2 also had circulating coccidioidal proteins. Using GSLIIaffinity enrichment, a total of 122 proteins and at least 2 peptideswere identified from 64 proteins (the peptide range was 1 to 17). On theother hand, sWGA affinity enrichment of plasma glycoproteins yielded atotal of 137 proteins (with a peptide range of 1 to 27). Among these, 97proteins were identified with at least 2 tryptic fragments. TABLE 4lists the ten most abundant coccidioidal proteins (those having thehighest spectral counts) in patient plasma. Patient 3 had only sevenfungal proteins present in plasma, which were identified by two or moretryptic fragments. Patients 4 and 5 had only two and three fungalproteins in circulation, respectively.

Among the three control plasma samples investigated with both GSLII andsWGA chromatography, single peptides were identified from 6 coccidioidalproteins. A protein identification can be made by the presence of asingle tryptic fragment/peptide (“one hit” protein entries), but if thetryptic fragment is not unique to the sequence of that protein, theconfidence in identification by mass spectrometry method as in thesestudies is low. FIG. 7 shows the proteins identified in two patientplasmas based on the presence of at least two tryptic peptides.

Coccidioides Proteins in Patient Urine: A urine sample collected from VFpatient 1 was enriched for glycoproteins using a sWGA lectin affinitycolumn. The eluate was trypsin digested (in-gel digestion) to reveal thepresence of ten coccidioidal proteins. Five of these proteins wereidentified by single unique peptides, while two or more peptides wereidentified from three different proteins. Two proteins were identifiedby the presence of six and five tryptic fragments, respectively. Amongthe ten proteins thus identified, four also were identified in a“control” urine sample obtained from a healthy donor. This includedhighly conserved proteins such as actin and ATP synthase. Three proteinswere uniquely present in urine from Patient 1 (and absent in plasma).These proteins included ADP ribosylation factor, a GTP binding proteinand ATP synthase beta subunit.

TABLE 4 Coccidioides proteins identified in patient (n = 2) plasma usingsWGA lectin chromatography and LC MS/MS. These fungal proteins wereidentified in patient plasma (with high spectral and peptide counts) andwere absent from control plasma. Percent sequence coverage signifies theextent of tryptic fragments identified from the protein sequence.Spectral Maximum Unique Protein ID count % coverage peptides5-methyltetrahydropteroyltriglutamate- 283 53 31 homocysteinemethyltransferase (CPSG_03208) malate dehydrogenase (CPAG_07192) 162 5213 O-acetylhomoserine 117 39 12 enolase (CPAG_04681) 76 55 15 vacuolarprotease A 72 40 8 peroxisomal matrix protein 71 64 7 endochitinase 1 7035 12 superoxide dismutase 59 72 8 heat shock 70 kDa protein 54 24 17formate dehydrogenase 51 31 9

Example 4—Lectin Enrichment of Coccidioides Glycans in Infected UrineUsing Agarose sWGA Column, and Detection by Mass Spectrometry Methods

Urine and CDN Ag Collection: Urine was retrospectively collected fromcompleted diagnostic specimens from the Mayo Clinic Arizona MicrobiologyDepartment. Coccidioidin (CDN Ag), a fungal lysate and culturesupernatant from in vitro grown mycelia of Coccidioides posadasii strainSilveira, was grown as described elsewhere (Grys et al., J Proteome Res15(10):3463-3472, 2016.)

Urine Lectin Chromatography and Glycan Extraction: 1 ml of urine or 20μg of CDN Ag was bound for 1 hour at room temperature onto 250 μl sWGAagarose beads (Vector Labs; Burlingham, Calif.) after equilibrating withConA buffer pH 8. Beads were washed three times with 2 ml ConA buffer(20 mM Tris, 500 mM NaCl, 1 mM CaCl₂, 1 mM MgCl₂, pH 7.4) and elutedtwice with 250 μl 4 M urea pH 4 for 5 minutes each, followed by a 100 μl0.5% trifluoroacetic acid elution. Six hundred (600) μl of 0.1 M Na₂PO₄buffer pH 7.2 was added to neutralize the acid and dilute the urea priorto deglycosylation. Two (2) μL of 2-mercaptoethanol was added to reducethe proteins prior to the addition of 50 U (units) of PNGase F (NewEngland Biolabs; Ipswich, Mass.) and incubated at 37° C. for 18 hours.The next day, the N-glycans were purified on a Hypercarb porousgraphitic carbon (PGC) cartridge (Thermo Scientific; Waltham, Mass.),according to the manufacturer's instructions.

LC MS/MS: Eluted glycans were speed vacuumed until dry and brought up inmobile phase A (0.1% FA in water) and loaded onto a Dionex ULTIMATE®3000 RSLC liquid chromatography system (Thermo) with a C18reversed-phase ion trap column. Peptides were separated using a 500nL/minute LC gradient comprised of 2%-60% B in 0-120 min. Mobile phase Awas 2% ACN in water with 0.1% FA and mobile phase B wasACN/methanol/water (80/10/10 by volume) with 0.1% FA. Eluting peptideswere analyzed using a Orbitrap Velos mass spectrometer (Thermo-Fisher)using collision-induced dissociation (CID) in positive ion mode. Theinstrument was configured to operate by data-dependent mode bycollecting MS1 data at 60,000 resolving power (measured at m/z 275) withan AGC value of 1E6 over a m/z range of 275-1800. Precursors werefragmented with normalized collision energy (NCE) of 35, and fragmentswere measured at 17,500 resolving power and a fixed first mass of 275.Resulting tandem MS/MS were collected on the top 20 precursor massespresent in each MS1 using an AGC value of 1E5, max ion fill time of 50ms, and an isolation window of 1.5 Da.

Glycan Analysis and Biomarker Determination: MS/MS spectra were analyzedusing SimGlycan v.5.60 (Premier Biosoft; Palo Alto, Calif.). Searchparameters were underivatized, free glycans in positive ion mode with Hand Na adducts. A 1 Da±0.5 Da error tolerance was allowed. Allglycosidic and cross-ring options were set to “yes”. Precursor m/zvalues were analyzed in Venny 2.1 (Oliveros (2007-2015), “Venny. Aninteractive tool for comparing lists with Venn's diagrams,” online atbioinfogp.cnb.csic.es/tools/venny/index.html) to determine shared andunique values amongst the samples.

Results

Based on clinical background, patients were placed into three diseasecategories (disseminated, acute pulmonary, and chronic pulmonary). Threepatients were determined to have disseminated disease, defined asconfirmed fungal infection at sites outside the pulmonary cavity; twopatients were determined to have acute pulmonary disease, defined asdisease confined to the pulmonary cavity with onset less than threemonths from sample collection; and one patient had chronic pulmonarydisease, defined as disease confined to the pulmonary cavity but withactive recurring disease and an initial onset of disease greater thanone year prior to sample collection. Six negative control urine samplesalso were included in the data analysis, and were collected fromindividuals with no symptoms. All results were compared against CDN Agto determine glycans that also were found in the in vitro grown mycelialphase of the fungus.

There were a number of unique precursor m/z values identified in thedifferent groups that were not found in any of the six negative controlurines. As shown in FIG. 9, many possible biomarker glycans wereidentified, of which some overlap between groups was seen. The first 50unique precursor m/z values of the glycans found in each group are shownin TABLE 5. Only the first 50 are listed in TABLE 5 due to spaceconstraints, and these are examples of the many biomarkers that can begenerated using the approach described herein. These m/z values arespecific to the method used, and the same biomarker may producedifferent m/z values depending on the preparation method andinstrumentation differences. However, those m/z values would not bepresent in subjects who do not have active coccidioidomycosis. Inpatients of unknown disease state, the detection of biomarkers (via m/zvalues) that are shared only with patients with provencoccidioidomycosis disease and/or shared with culture lysates ofCoccidioides, is evidence for diagnosis of coccidioidomycosis.

TABLE 5 The first 50 unique precursor m/z values of glycans found inthree Coccidioidomycosis patient categories (acute, chronic, anddisseminated), controls, and culture lysates Exclu- Common in Exclu-Exclu- sively in Exclu- Common in Common in Common in Dissem- sively insively in Chronic sively in Dissem- Common in Acute; Common in Common inDissem- inated, Dissem- Acute Pulmonary CDN Ag inated Acute and Chronicand Chronic and Acute and inated and Acute and inated Pulmonary (n = (n= and Acute Chronic CDN Ag CDN Ag CDN Ag CDN Ag CDN Ag (n = 45) (n =594) 16,303) 13,090) (n = 6) (n = 5) (n = 2) (n = 286) (n = 84) (n = 5)(n = 3) 1043.49 767 391.284 817 1077.7371 307.113 712.992 419.315 705317.682 302.653 1245.249 1043.769 559.7 1511 394.796 307.112 499.2591287.001 786.041 377.228 411.212 322.692 969.041 542.703 218.884 457.71573.267 322.822 838.372 525.289 557.297 333.7 1389.89 400.74 1022.087536.258 970.39 786.851 811.273 540.752 344.698 823.189 590.696 516.313716.31 482.171 376.899 678.323 548.75 350.68 546.838 752.6 432.225865.908 687.323 868.78 727.333 393.188 1321.946 822.432 391.885 283.263567.788 398.196 1264.472 1288.9189 540.772 1056.834 701.294 408.711295.801 400.799 637.333 859.764 730.015 409.717 960.586 486.738 583.86982.714 520.24 420.181 1266.214 290.85 1149.586 737.305 419.209 422.251948.789 705.591 352.531 980.686 563.773 460.219 575.821 376.771 535.286570.302 475.26 462.281 981.279 406.828 344.545 1403.6689 775.367 492.7541099.725 593.157 1021.589 1160.661 693.939 492.755 980.1 416.794 781.365775.826 648.284 498.222 874.787 1435.3621 629.354 718.322 768.359500.739 1000.766 422.758 567.282 1104.1281 735.33 511.762 1383.705366.805 362.518 452.87 804.352 521.278 789.336 667.176 1062.606 1240.04440.226 546.836 799.138 1320.896 1037.069 1175.6801 833.373 553.3171029.212 1533.803 1110.613 434.882 448.203 554.234 1168.738 566.741050.593 1042.697 655.302 570.808 1341.635 1336.9091 1558.905 1144.616628.967 578.25 1452.635 681.693 358.534 611.806 625.296 578.7971280.1071 350.81 1110.11 994.72 696.627 595.298 1330.099 1190.4561694.293 986.749 586.278 595.81 1312.524 607.209 521.759 1078.691 702.66659.341 −1243.041 586.675 484.266 937.771 499.755 661.307 343.0571739.684 567.36 1257.015 1029.939 666.794 840.724 450.799 480.8 658.826574.795 675.327 751.002 1799.54 727.872 712.318 804.369 688.268 680.968536.154 585.798 1156.7629 743.82 691.381 473.237 284.832 1568.9081034.248 645.618 712.837 879.873 408.768 664.397 1739.783 455.239714.346 586.918 1356.827 758.489 998.447 379.191 738.669 699.9761602.7581 803.427 1016.705 589.261 776.36 908.384 454.695 443.58 697.352768.354 779.366 984.316 1749.298 472.287 713.347 679.238 780.708 957.708448.73 361.185 801.364 646.811 865.611 768.997 536.675 689.875 726.011785.705 918.428 617.63 506.755 1000.074 627.839 356.653 924.99 699.3151154.475 1102.1071 309.063 349.659 980.028 795.331 308.88 786.408695.338 771.386 980.851 635.706 1025.058 776.912 686.424 524.757 732.315522.751 1058.582 904.954 889.388 447.727 504.749 622.801 879.445 732.818739.654 596.651 999.573 809.816 567.294 1042.308 1479.866 711.888744.841 796.847 564.227 1205.05 1029.08 1025.964 891.903

Other Embodiments

It is to be understood that while the invention has been described inconjunction with the detailed description thereof, the foregoingdescription is intended to illustrate and not limit the scope of theinvention, which is defined by the scope of the appended claims. Otheraspects, advantages, and modifications are within the scope of thefollowing claims.

What is claimed is:
 1. A method for altering the treatment of a subjectpresenting with, and optionally undergoing antibacterial or anti-viraltreatment for, one or more symptoms of community-acquired pneumonia, ora subject with one or more symptoms of invasive fungal infection, themethod comprising: enriching for one or more antigens of Coccidioidesimmitis or Coccidioides posadasii in a body fluid sample from thesubject, wherein the enriching comprises lectin-based enrichment of C.immitis or C. posadasii antigens, and wherein the lectin comprisessuccinylated Wheat Germ Agglutinin (sWGA), Griffonia simplicifolia IIlectin (GSLII), or Wheat Germ Agglutinin (WGA); detecting one or more ofthe enriched antigens or their components; and stopping theantibacterial or anti-viral treatment, initiating antifungal treatment,or stopping the antibacterial or anti-viral treatment and initiatingantifungal treatment.
 2. The method of claim 1, wherein the antifungaltreatment comprises administration of fluconazole, ketoconazole,itraconazole, voriconazole, posaconazole, isavuconazole, oramphotericin.
 3. The method of claim 1, wherein the detecting comprisesusing mass spectrometry.
 4. The method of claim 1, wherein the enrichingfurther comprises lectin-based enrichment of C. immitis or C. posadasiiantigens using one or more additional lectins that bind to both humanand Coccidioides antigens.
 5. The method of claim 4, wherein the one ormore additional lectins comprise one or more of Concanavalin A (Con A),Erythrina crystagalli Lectin (ECL), and Pisum sativum Agglutinin (PSA).6. The method of claim 1, wherein the enriching further compriseslectin-based enrichment of C. immitis or C. posadasii antigens, andwherein the additional lectin binds to human antigens and enrichesCoccidioides antigens by reducing the number or percentage of humanantigens present in the body fluid from the subject.
 7. The method ofclaim 6, wherein the additional lectin comprises one or more ofConcanavalin A (Con A), Datura stramonium Lectin (DSL), Erythrinacrystagalli Lectin (ECL), Griffonia simplicifolia Lectin I (GSLI),Jacalin (JAC), Len culinaris Lectin (LCA), Peanut Agglutinin (PNA),Phaseolus vulgaris Erythroagglutinin (PVE), Phaseolus vulgarisLeukoagglutinin (PVL), Pisum sativum Agglutinin (PSA), Ricinus communisAgglutinin (RCA I), Solanum tuberosum Lectin (STL), Soybean Agglutinin(SBA), Ulex europaeus Agglutinin I (UEA I), and Vicia villosa Lectin(VVL).